Aedes aegypti mosquitoes are resistant to various insecticides, including pyrethroids, throughout Thailand. We previously reported that Ae. aegypti from Mae Wong district, Nakhon Sawan Province in north-central Thailand, were resistant to insecticides, including pyrethroids (deltamethrin and permethrin), organophosphates and carbamates, and that high levels of detoxification enzymes were present. In the present study we used the method of suppression by subtractive hybridization to determine differential expression of genes in Mae Wong Ae. aegypti that survived the exposure to increasing doses (∼ 1.5 - 2 × 10^-5M) of deltamethrin beyond the diagnostic dose compared to unexposed mosquitoes. Screening of 350 cDNA clones from the suppression subtractive library by cDNA array hybridization revealed that 58 clones were over-expressed in the mosquito that survived high dose deltamethrin. The over-expressed cDNA insert sequences corresponded to 11 functional genes, five hypothetical protein genes, and five sequences of unknown function that could be located on the supercontig of the Ae. aegypti genome. The functional genes are those coding for cuticular proteins, muscle proteins, proteins related to controlling the release of synaptic vesicles, and other genes such as heat shock protein and small subunit ribosomal RNA. Over-expression of tomosyn and myosin light chain kinase genes was verified using a semiquantitative reverse transcription-polymerase chain reaction (RT-PCR), confirming their increased expression in response to deltamethrin exposure in insecticide-resistant Ae. aegypti.